Preliminary data exploration
Contaminant ASVs were identified with the prevalence method using the decontam package.
Plant measures overview
Scaled-centered plant ‘health’ measures, broken down by treatment factors.
Model output
Formula:value ~ drought * host * fire_freq + (1|inoculum_site/block))
| effect | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|
| fixed | (Intercept) | 0.071 | 0.280 | 0.255 | 5.343 | 0.808 |
| fixed | droughtND | -0.017 | 0.163 | -0.106 | 384.262 | 0.916 |
| fixed | hostCeanothus velutinus | -0.522 | 0.164 | -3.190 | 381.647 | 0.002 |
| fixed | fire_freq | 0.104 | 0.154 | 0.675 | 5.360 | 0.528 |
| fixed | droughtND:hostCeanothus velutinus | 0.560 | 0.232 | 2.412 | 383.262 | 0.016 |
| fixed | droughtND:fire_freq | -0.037 | 0.089 | -0.416 | 381.323 | 0.677 |
| fixed | hostCeanothus velutinus:fire_freq | -0.002 | 0.090 | -0.017 | 382.464 | 0.987 |
| fixed | droughtND:hostCeanothus velutinus:fire_freq | -0.033 | 0.127 | -0.263 | 382.083 | 0.793 |
Inoculum communities overview
Taxonomic overview
Bacteria
Alpha diversity
Effect of Shannon diversity on plant measures
| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | -0.733 | 0.476 | -1.541 | 360.365 | 0.124 |
| fixed | NA | Shannon | 0.129 | 0.085 | 1.514 | 664.977 | 0.130 |
| fixed | NA | hostCeanothus velutinus | 0.898 | 0.708 | 1.269 | 664.182 | 0.205 |
| fixed | NA | droughtND | 0.448 | 1.182 | 0.379 | 678.507 | 0.705 |
| fixed | NA | fire_freq | 1.654 | 0.563 | 2.938 | 668.475 | 0.003 |
| fixed | NA | Shannon:hostCeanothus velutinus | -0.163 | 0.125 | -1.304 | 658.644 | 0.193 |
| fixed | NA | Shannon:droughtND | -0.088 | 0.212 | -0.415 | 678.004 | 0.678 |
| fixed | NA | hostCeanothus velutinus:droughtND | 0.379 | 1.959 | 0.193 | 696.563 | 0.847 |
| fixed | NA | Shannon:fire_freq | -0.282 | 0.100 | -2.824 | 677.140 | 0.005 |
| fixed | NA | hostCeanothus velutinus:fire_freq | -3.494 | 1.363 | -2.564 | 681.500 | 0.011 |
| fixed | NA | droughtND:fire_freq | -1.120 | 0.838 | -1.336 | 673.807 | 0.182 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | -0.070 | 0.344 | -0.203 | 696.859 | 0.839 |
| fixed | NA | Shannon:hostCeanothus velutinus:fire_freq | 0.597 | 0.221 | 2.696 | 683.713 | 0.007 |
| fixed | NA | Shannon:droughtND:fire_freq | 0.196 | 0.151 | 1.301 | 672.746 | 0.194 |
| fixed | NA | hostCeanothus velutinus:droughtND:fire_freq | 3.048 | 1.773 | 1.719 | 687.380 | 0.086 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:fire_freq | -0.521 | 0.293 | -1.777 | 690.349 | 0.076 |
| ran_pars | inoculum_site:block | sd__(Intercept) | 0.296 | NA | NA | NA | NA |
| ran_pars | block | sd__(Intercept) | 0.332 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.895 | NA | NA | NA | NA |
Fungi
Alpha diversity
Effect of Shannon diversity on plant measures
| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | 0.123 | 0.274 | 0.448 | 71.682 | 0.656 |
| fixed | NA | Shannon | -0.172 | 0.181 | -0.954 | 621.589 | 0.341 |
| fixed | NA | hostCeanothus velutinus | 0.192 | 0.513 | 0.374 | 612.037 | 0.708 |
| fixed | NA | droughtND | 0.203 | 0.310 | 0.654 | 697.861 | 0.513 |
| fixed | NA | fire_freq | 0.200 | 0.198 | 1.010 | 526.205 | 0.313 |
| fixed | NA | Shannon:hostCeanothus velutinus | -0.049 | 0.340 | -0.144 | 582.109 | 0.886 |
| fixed | NA | Shannon:droughtND | -0.251 | 0.275 | -0.911 | 701.406 | 0.363 |
| fixed | NA | hostCeanothus velutinus:droughtND | -0.492 | 0.609 | -0.807 | 676.824 | 0.420 |
| fixed | NA | Shannon:fire_freq | -0.087 | 0.152 | -0.571 | 613.249 | 0.568 |
| fixed | NA | hostCeanothus velutinus:fire_freq | -0.178 | 0.420 | -0.425 | 635.728 | 0.671 |
| fixed | NA | droughtND:fire_freq | -0.215 | 0.230 | -0.933 | 689.863 | 0.351 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | 0.387 | 0.439 | 0.881 | 681.222 | 0.379 |
| fixed | NA | Shannon:hostCeanothus velutinus:fire_freq | 0.159 | 0.244 | 0.652 | 623.003 | 0.515 |
| fixed | NA | Shannon:droughtND:fire_freq | 0.187 | 0.192 | 0.974 | 687.152 | 0.330 |
| fixed | NA | hostCeanothus velutinus:droughtND:fire_freq | 0.217 | 0.472 | 0.459 | 675.089 | 0.646 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:fire_freq | -0.285 | 0.304 | -0.940 | 682.735 | 0.348 |
| ran_pars | inoculum_site:block | sd__(Intercept) | 0.264 | NA | NA | NA | NA |
| ran_pars | block | sd__(Intercept) | 0.334 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.901 | NA | NA | NA | NA |
Comparison between inoculum and root communities
Bacteria
Not all taxa in the inoculae were subsequently found in the root samples
Fungi
Microbial guilds
Bacteria
I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:
| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | -0.8572 | 0.2935 | -2.9206 | 49.6839 | 0.0052 | Ceanothus |
| fixed | proportion_pathogen | 1.5096 | 0.6362 | 2.3727 | 410.9860 | 0.0181 | Ceanothus |
| fixed | droughtND | 1.1837 | 0.3866 | 3.0617 | 408.2273 | 0.0023 | Ceanothus |
| fixed | fire_freq | 0.2444 | 0.1865 | 1.3108 | 407.9500 | 0.1907 | Ceanothus |
| fixed | proportion_pathogen:droughtND | -2.0673 | 1.1062 | -1.8689 | 409.0361 | 0.0624 | Ceanothus |
| fixed | proportion_pathogen:fire_freq | -0.2759 | 0.5126 | -0.5383 | 408.5644 | 0.5906 | Ceanothus |
| fixed | droughtND:fire_freq | 0.0513 | 0.2604 | 0.1968 | 409.6223 | 0.8441 | Ceanothus |
| fixed | proportion_pathogen:droughtND:fire_freq | -0.5892 | 0.7795 | -0.7558 | 410.0850 | 0.4502 | Ceanothus |
| fixed | (Intercept) | -0.6413 | 0.4190 | -1.5306 | 66.8098 | 0.1306 | Abies |
| fixed | proportion_pathogen | 1.8993 | 1.1867 | 1.6005 | 487.9044 | 0.1101 | Abies |
| fixed | droughtND | 0.9255 | 0.4772 | 1.9394 | 489.1544 | 0.0530 | Abies |
| fixed | fire_freq | 0.3495 | 0.1975 | 1.7700 | 486.3527 | 0.0773 | Abies |
| fixed | proportion_pathogen:droughtND | -2.8146 | 1.4874 | -1.8923 | 488.8933 | 0.0590 | Abies |
| fixed | proportion_pathogen:fire_freq | -0.8519 | 0.7193 | -1.1845 | 486.3072 | 0.2368 | Abies |
| fixed | droughtND:fire_freq | -0.4264 | 0.2898 | -1.4712 | 486.9375 | 0.1419 | Abies |
| fixed | proportion_pathogen:droughtND:fire_freq | 1.1320 | 0.9384 | 1.2063 | 486.9307 | 0.2283 | Abies |
Fungi
How does the proportion of mutualist fungi relate to indicators of plant health?
In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.
We see an opposite pattern when looking at the proportions of putatively pathogenic fungi
| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | -0.1914 | 0.1861 | -1.0288 | 12.3567 | 0.3233 | Ceanothus |
| fixed | proportion_pathogen | -0.8657 | 0.4922 | -1.7586 | 407.2118 | 0.0794 | Ceanothus |
| fixed | droughtND | 0.4250 | 0.1620 | 2.6238 | 407.5730 | 0.0090 | Ceanothus |
| fixed | fire_freq | 0.1795 | 0.0826 | 2.1721 | 408.1123 | 0.0304 | Ceanothus |
| fixed | proportion_pathogen:droughtND | -0.0517 | 0.7572 | -0.0683 | 410.3794 | 0.9456 | Ceanothus |
| fixed | proportion_pathogen:fire_freq | -0.0294 | 0.2703 | -0.1087 | 408.7904 | 0.9135 | Ceanothus |
| fixed | droughtND:fire_freq | -0.1092 | 0.1029 | -1.0610 | 408.9926 | 0.2893 | Ceanothus |
| fixed | proportion_pathogen:droughtND:fire_freq | -0.5012 | 0.5492 | -0.9126 | 410.9484 | 0.3620 | Ceanothus |
| fixed | (Intercept) | -0.0252 | 0.2310 | -0.1090 | 7.9855 | 0.9159 | Abies |
| fixed | proportion_pathogen | -0.8837 | 0.5533 | -1.5972 | 487.2401 | 0.1109 | Abies |
| fixed | droughtND | 0.1040 | 0.1283 | 0.8108 | 487.2950 | 0.4179 | Abies |
| fixed | fire_freq | 0.0964 | 0.0538 | 1.7910 | 484.7280 | 0.0739 | Abies |
| fixed | proportion_pathogen:droughtND | 0.0805 | 0.6645 | 0.1212 | 487.6918 | 0.9036 | Abies |
| fixed | proportion_pathogen:fire_freq | 0.2447 | 0.2306 | 1.0613 | 485.8624 | 0.2891 | Abies |
| fixed | droughtND:fire_freq | -0.1060 | 0.0721 | -1.4694 | 484.9722 | 0.1424 | Abies |
| fixed | proportion_pathogen:droughtND:fire_freq | -0.0540 | 0.3846 | -0.1404 | 485.4858 | 0.8884 | Abies |
| fixed | (Intercept) | -0.3606 | 0.2168 | -1.6636 | 17.0196 | 0.1145 | Ceanothus |
| fixed | proportion_mutualist | 0.0227 | 0.2761 | 0.0822 | 408.2311 | 0.9345 | Ceanothus |
| fixed | droughtND | 0.4699 | 0.2285 | 2.0564 | 407.7090 | 0.0404 | Ceanothus |
| fixed | fire_freq | 0.1075 | 0.0744 | 1.4441 | 407.1394 | 0.1495 | Ceanothus |
| fixed | proportion_mutualist:droughtND | -0.0395 | 0.4118 | -0.0960 | 408.5606 | 0.9236 | Ceanothus |
| fixed | proportion_mutualist:fire_freq | 0.2470 | 0.2528 | 0.9768 | 408.2959 | 0.3293 | Ceanothus |
| fixed | droughtND:fire_freq | -0.1153 | 0.1154 | -0.9991 | 407.9088 | 0.3184 | Ceanothus |
| fixed | proportion_mutualist:droughtND:fire_freq | -0.1034 | 0.3093 | -0.3345 | 409.0122 | 0.7382 | Ceanothus |
| fixed | (Intercept) | -0.7047 | 0.2849 | -2.4733 | 19.8113 | 0.0226 | Abies |
| fixed | proportion_mutualist | 0.9018 | 0.2626 | 3.4342 | 487.8720 | 0.0006 | Abies |
| fixed | droughtND | 0.4584 | 0.2768 | 1.6561 | 488.7631 | 0.0984 | Abies |
| fixed | fire_freq | 0.3142 | 0.0919 | 3.4196 | 487.1292 | 0.0007 | Abies |
| fixed | proportion_mutualist:droughtND | -0.6042 | 0.3647 | -1.6569 | 489.4817 | 0.0982 | Abies |
| fixed | proportion_mutualist:fire_freq | -0.2953 | 0.1455 | -2.0295 | 487.4639 | 0.0429 | Abies |
| fixed | droughtND:fire_freq | -0.3247 | 0.1468 | -2.2124 | 488.1415 | 0.0274 | Abies |
| fixed | proportion_mutualist:droughtND:fire_freq | 0.3414 | 0.2081 | 1.6404 | 488.5207 | 0.1016 | Abies |
Beta-Diversity
Bacteria
| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 3.8414120 | 0.0687480 | 11.063965 | 0.001 |
| fire_freq | 1 | 1.7434756 | 0.0312022 | 5.021527 | 0.001 |
| drought | 1 | 0.8088162 | 0.0144750 | 2.329538 | 0.001 |
| host:fire_freq | 1 | 0.7153777 | 0.0128028 | 2.060418 | 0.002 |
| host:drought | 1 | 0.7562988 | 0.0135351 | 2.178278 | 0.002 |
| fire_freq:drought | 1 | 0.3814427 | 0.0068265 | 1.098624 | 0.234 |
| host:fire_freq:drought | 1 | 0.4106606 | 0.0073494 | 1.182777 | 0.162 |
| Residual | 136 | 47.2192419 | 0.8450610 | NA | NA |
| Total | 143 | 55.8767255 | 1.0000000 | NA | NA |
Fungi
| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 1.9352113 | 0.0300393 | 4.6753844 | 0.001 |
| fire_freq | 1 | 3.4231420 | 0.0531356 | 8.2701587 | 0.001 |
| drought | 1 | 0.5712680 | 0.0088675 | 1.3801580 | 0.113 |
| host:fire_freq | 1 | 0.9705051 | 0.0150646 | 2.3446971 | 0.003 |
| host:drought | 1 | 0.3803731 | 0.0059043 | 0.9189645 | 0.583 |
| fire_freq:drought | 1 | 0.5128794 | 0.0079612 | 1.2390938 | 0.202 |
| host:fire_freq:drought | 1 | 0.3369443 | 0.0052302 | 0.8140424 | 0.746 |
| Residual | 136 | 56.2924276 | 0.8737973 | NA | NA |
| Total | 143 | 64.4227507 | 1.0000000 | NA | NA |
Important Taxa
These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables
Bacteria
Differential Abundance
Relative Abundances of ‘important’ taxa in root samples
Fungi
Differential Abundance
No fungal taxa were found to have significant differential abundance between drought levels
Relative Abundances of ‘important’ taxa in root samples
Phylogenetic properties
Bacteria
- Still kind of messy
- What specific questions do we need to address with this?
Fungi
- Phylogenetic dispersion is tricky with ITS markers :(
- Could try GhostTree for fungi of interest that come up as ‘unknown’
Network properties
Do we want to get into this in this paper?
Bacteria
Fungi
Cross-Domain
_____
Soil chemistry
Overview of soil properties for each inoculum source:
Testing for significant differences between the samples…
Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| Mn | 1.248 | 0.268 | 4.658 | 0.000 |
| NH4 | 0.770 | 0.268 | 2.875 | 0.004 |
| Fe:inoc_site1 | 1.516 | 0.328 | 4.618 | 0.000 |
| K:inoc_site1 | 0.904 | 0.328 | 2.753 | 0.006 |
| NO3:inoc_site1 | -0.793 | 0.328 | -2.417 | 0.016 |
| TKN:inoc_site1 | 0.735 | 0.328 | 2.240 | 0.026 |
| Zn:inoc_site1 | 1.160 | 0.328 | 3.536 | 0.000 |
| Fe:inoc_site2 | 0.831 | 0.328 | 2.532 | 0.012 |
| K:inoc_site2 | 0.801 | 0.328 | 2.440 | 0.015 |
| Mn:inoc_site2 | -1.081 | 0.328 | -3.294 | 0.001 |
| TKN:inoc_site2 | 0.660 | 0.328 | 2.010 | 0.045 |
| Mn:inoc_site3 | -1.526 | 0.328 | -4.648 | 0.000 |
| NH4:inoc_site3 | -0.976 | 0.328 | -2.973 | 0.003 |
| Zn:inoc_site3 | -0.693 | 0.328 | -2.112 | 0.035 |
| C:N:inoc_site4 | -0.893 | 0.328 | -2.721 | 0.007 |
| EC:inoc_site4 | -1.026 | 0.328 | -3.127 | 0.002 |
| Mn:inoc_site4 | -1.349 | 0.328 | -4.110 | 0.000 |
| B:inoc_site5 | 1.369 | 0.328 | 4.171 | 0.000 |
| Ca:inoc_site5 | 1.192 | 0.328 | 3.631 | 0.000 |
| K:inoc_site5 | 0.683 | 0.328 | 2.080 | 0.038 |
| Mg:inoc_site5 | 0.682 | 0.328 | 2.078 | 0.039 |
| Mn:inoc_site5 | -1.099 | 0.328 | -3.350 | 0.001 |
| NO3:inoc_site5 | 1.854 | 0.328 | 5.649 | 0.000 |
| TKN:inoc_site5 | 1.022 | 0.328 | 3.114 | 0.002 |
| Zn:inoc_site5 | 1.448 | 0.328 | 4.412 | 0.000 |
| B:inoc_site6 | 0.918 | 0.328 | 2.798 | 0.005 |
| Mn:inoc_site6 | -1.535 | 0.328 | -4.678 | 0.000 |
| NH4:inoc_site6 | -0.754 | 0.328 | -2.299 | 0.022 |
| NO3:inoc_site6 | 1.273 | 0.328 | 3.880 | 0.000 |
| Zn:inoc_site6 | 1.290 | 0.328 | 3.932 | 0.000 |